PMID- 28177307
OWN - NLM
STAT- MEDLINE
DCOM- 20171025
LR  - 20171025
IS  - 2059-7983 (Electronic)
IS  - 2059-7983 (Linking)
VI  - 73
IP  - Pt 2
DP  - 2017 Feb 1
TI  - AceDRG: a stereochemical description generator for ligands.
PG  - 112-122
LID - 10.1107/S2059798317000067 [doi]
AB  - The program AceDRG is designed for the derivation of stereochemical information
      about small molecules. It uses local chemical and topological environment-based
      atom typing to derive and organize bond lengths and angles from a small-molecule 
      database: the Crystallography Open Database (COD). Information about the
      hybridization states of atoms, whether they belong to small rings (up to
      seven-membered rings), ring aromaticity and nearest-neighbour information is
      encoded in the atom types. All atoms from the COD have been classified according 
      to the generated atom types. All bonds and angles have also been classified
      according to the atom types and, in a certain sense, bond types. Derived data are
      tabulated in a machine-readable form that is freely available from CCP4. AceDRG
      can also generate stereochemical information, provided that the basic bonding
      pattern of a ligand is known. The basic bonding pattern is perceived from one of 
      the computational chemistry file formats, including SMILES, mmCIF, SDF MOL and
      SYBYL MOL2 files. Using the bonding chemistry, atom types, and bond and angle
      tables generated from the COD, AceDRG derives the `ideal' bond lengths, angles,
      plane groups, aromatic rings and chirality information, and writes them to an
      mmCIF file that can be used by the refinement program REFMAC5 and the
      model-building program Coot. Other refinement and model-building programs such as
      PHENIX and BUSTER can also use these files. AceDRG also generates one or more
      coordinate sets corresponding to the most favourable conformation(s) of a given
      ligand. AceDRG employs RDKit for chemistry perception and for initial
      conformation generation, as well as for the interpretation of SMILES strings, SDF
      MOL and SYBYL MOL2 files.
FAU - Long, Fei
AU  - Long F
AD  - Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue,
      Cambridge CB2 0QH, England.
FAU - Nicholls, Robert A
AU  - Nicholls RA
AD  - Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue,
      Cambridge CB2 0QH, England.
FAU - Emsley, Paul
AU  - Emsley P
AD  - Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue,
      Cambridge CB2 0QH, England.
FAU - Graaeulis, Saulius
AU  - Graaeulis S
AD  - Institute of Biotechnology, Sauletekio al. 7, LT-10257 Vilnius, Lithuania.
FAU - Merkys, Andrius
AU  - Merkys A
AD  - Institute of Biotechnology, Sauletekio al. 7, LT-10257 Vilnius, Lithuania.
FAU - Vaitkus, Antanas
AU  - Vaitkus A
AD  - Institute of Biotechnology, Sauletekio al. 7, LT-10257 Vilnius, Lithuania.
FAU - Murshudov, Garib N
AU  - Murshudov GN
AD  - Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue,
      Cambridge CB2 0QH, England.
LA  - eng
PT  - Journal Article
DEP - 20170201
PL  - United States
TA  - Acta Crystallogr D Struct Biol
JT  - Acta crystallographica. Section D, Structural biology
JID - 101676043
RN  - 0 (Bacterial Proteins)
RN  - 0 (EthR protein, Mycobacterium tuberculosis)
RN  - 0 (Ligands)
RN  - 0 (Repressor Proteins)
RN  - 0 (Small Molecule Libraries)
RN  - EC 5.4.- (Intramolecular Transferases)
RN  - EC 5.4.99.9 (UDP-galactopyranose mutase)
SB  - IM
MH  - Bacterial Proteins/chemistry/metabolism
MH  - Binding Sites
MH  - Crystallography, X-Ray
MH  - Databases, Factual
MH  - Deinococcus/chemistry/metabolism
MH  - Intramolecular Transferases/chemistry/metabolism
MH  - Ligands
MH  - Models, Molecular
MH  - Molecular Conformation
MH  - Mycobacterium tuberculosis/chemistry/metabolism
MH  - Repressor Proteins/chemistry/metabolism
MH  - Small Molecule Libraries/*chemistry/metabolism
MH  - *Software
MH  - Stereoisomerism
PMC - PMC5297914
OTO - NOTNLM
OT  - AceDRG
OT  - Crystallography Open Database
OT  - RDKit
OT  - ligand chemistry
OT  - refinement
EDAT- 2017/02/09 06:00
MHDA- 2017/10/27 06:00
CRDT- 2017/02/09 06:00
PHST- 2016/09/29 00:00 [received]
PHST- 2017/01/03 00:00 [accepted]
PHST- 2017/02/09 06:00 [entrez]
PHST- 2017/02/09 06:00 [pubmed]
PHST- 2017/10/27 06:00 [medline]
AID - S2059798317000067 [pii]
AID - 10.1107/S2059798317000067 [doi]
PST - ppublish
SO  - Acta Crystallogr D Struct Biol. 2017 Feb 1;73(Pt 2):112-122. doi:
      10.1107/S2059798317000067. Epub 2017 Feb 1.

PMID- 22505262
OWN - NLM
STAT- MEDLINE
DA  - 20120416
DCOM- 20120619
LR  - 20141016
IS  - 1399-0047 (Electronic)
IS  - 0907-4449 (Linking)
VI  - 68
IP  - Pt 4
DP  - 2012 Apr
TI  - Handling ligands with Coot.
PG  - 425-30
LID - 10.1107/S0907444912000200 [doi]
AB  - Coot is a molecular-graphics application primarily aimed to assist in model
      building and validation of biological macromolecules. Recently, tools have been
      added to work with small molecules. The newly incorporated tools for the
      manipulation and validation of ligands include interaction with PRODRG, subgraph 
      isomorphism-based tools, representation of ligand chemistry, ligand fitting and
      analysis, and are described here.
FAU - Debreczeni, Judit E
AU  - Debreczeni JE
AD  - Structure and Biophysics, DS, AstraZeneca, Alderley Park SK10 4TG, England.
      judit.debreczeni@astrazeneca.com
FAU - Emsley, Paul
AU  - Emsley P
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20120316
PL  - United States
TA  - Acta Crystallogr D Biol Crystallogr
JT  - Acta crystallographica. Section D, Biological crystallography
JID - 9305878
RN  - 0 (Ligands)
SB  - IM
MH  - Crystallography, X-Ray/*methods
MH  - Ligands
MH  - Models, Molecular
MH  - Software
PMC - PMC3322601
OID - NLM: PMC3322601
EDAT- 2012/04/17 06:00
MHDA- 2012/06/20 06:00
CRDT- 2012/04/17 06:00
PHST- 2011/08/25 [received]
PHST- 2012/01/03 [accepted]
PHST- 2012/03/16 [epublish]
AID - S0907444912000200 [pii]
AID - 10.1107/S0907444912000200 [doi]
PST - ppublish
SO  - Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):425-30. doi:
      10.1107/S0907444912000200. Epub 2012 Mar 16.
